Strengths and considerations
- Defines complementary tasks around the same measurement modality.pluskal-lab/MassSpecGym official source · README: opening challenge list; Getting started with MassSpecGym
benchmark · task
MassSpecGym Molecule retrieval
Rank candidate molecules for a tandem mass spectrum.
At a glance
Explanatory profile: limited source coverage · Automated source review, 2026-09-16. This does not change the review status of its results.
| Property | Description and evidence |
|---|---|
| Record type | Component taskpluskal-lab/MassSpecGym official source · README: opening challenge list; Getting started with MassSpecGym |
| Inputs | MS/MS spectrum and a defined candidate setpluskal-lab/MassSpecGym official source · README: opening challenge list; Getting started with MassSpecGym |
| Outputs and assessment | Candidate rankingpluskal-lab/MassSpecGym official source · README: opening challenge list; Getting started with MassSpecGym |
| Datasets | Not extracted or verified for this record. |
| Organisms | Not extracted or verified for this record. |
| Assays | Not extracted or verified for this record. |
| Splits | Not extracted or verified for this record. |
| Adaptation | Not extracted or verified for this record. |
| Baselines | Not extracted or verified for this record. |
How it works
Conceptual component-task overview. Exact data versions, split files and scorer settings must be taken from the source.
Read the diagram as text
- MS/MS spectrum and a defined candidate set
- MassSpecGym Molecule retrieval
- Candidate ranking
Procedure
This is the MassSpecGym Molecule retrieval component, not the parent suite as a whole. Choose de novo generation, candidate retrieval or spectrum simulation. Each challenge specifies its input information, splits and output scoring; formula-assisted settings are separate variants.
pluskal-lab/MassSpecGym official source · README: opening challenge list; Getting started with MassSpecGymConnected tasks and protocols
- MassSpecGym · suite · part of
These associations do not imply identical protocols or interchangeable scores.
Tested models and results
Release 2026-09-16-d74d282221a9 · 0 evaluations · 0 metric rows. Different protocols are not a single leaderboard.
No evaluations linked in this release.
Strengths and limitations
Limitations and conditions
- Chemical-formula assistance changes available information; tasks and assisted variants cannot be collapsed into one score.pluskal-lab/MassSpecGym official source · README: opening challenge list; Getting started with MassSpecGym
Profile review details
Existing catalogue evidence and cited extraction inspected. The specific protocol gaps listed here remain unresolved; numerical source checks do not constitute complete methods review.
Stable record: discovery-benchmark-massspecgym-molecule-retrievalApplicable tests and references
Applicability is distinct from a completed evaluation.
- Mass spectral cosine matching · proposed
Sources and history
Release 2026-09-16-d74d282221a9 · Record review: discovered
- pluskal-lab/MassSpecGym official source · Original source · f259fe3780d5bd227fc6ece36ce6f397c2eef716
Technical metadata and extraction receipts
Stable ID: discovery-benchmark-massspecgym-molecule-retrieval
- areas
- metabolomics
- entity level
- task
- missing metadata
- dataset release: unextracted; metric implementation: unextracted; split manifest: unextracted; version: unextracted
- scope note
- Specialist molecular or omics evaluation; protocol details require review before numerical comparison.
- task
- Rank candidate structures from a tandem mass spectrum
- version
- Not reported
Related records
- parent: MassSpecGym
- part of: MassSpecGym
- applicable to: Mass spectral cosine matching
- subject: MassSpecGym Molecule retrieval: part of MassSpecGym